Build BSgenome by youself

Build a BSgenome by youself

Reference: Tom Guest

In this tutorial, I’ll show how to create a BSgenome library with Linux commands. The main steps for doing this are to prepare the fasta files and the configure files.

Preparing the sequence files and configuring file

We’d like to store each chromosome into an independent file and record them in a configuring file so the BSgenome can find them. Here I use awk to remove useless information in the name and seqkit to extract seqs.
Prepare: Genome.fa and seqkit
conda install -c bioconda seqkit

mkdir BSgenome # make a new directory
cd BSgenome    # Enter the directory
awk '{print $1}' ../Genome.fa > sample.fa   # samplify the name of each sequence
grep ">" sample.fa | sed 's/>//'> list.txt               # Get the name sequences

for i in $(cat list.txt)
do echo -e $i"\n"$i"\n"$i"\n"$i"\n" > tmp
    seqkit grep -n -f tmp  sample.fa > $i.fa
done

rm sample.fa  list.txt tmp

echo 'Package: BSgenome.dme.BDGP6.32
Title: Full genome sequence
Description: Full genome sequence
Version: 1.0.0
organism: drosophila melanogaster
common_name: fruit fly
provider: BDGP
provider_version: 6.32
release_date: ?
release_name: ?
source_url: ?
organism_biocview: ?
BSgenomeObjname: dme
seqnames: c("2L", "2R", "3L", "3R", "4", "EGFP", "GAL4", "mCD8GFP", "mitochondrion_genome", "test", "X", "Y")
seqs_srcdir: /media/ken/BackUP/Drosophila/BSgenome
' > BSgenome.dme.BDGP6.32-seed

R

library(BSgenome)
forgeBSgenomeDataPkg("BSgenome.dme.BDGP6.32-seed")

If everything is right, you would see the codes below and a directory BSgenome.dme.BDGP6.32 was created. Now, we need to package it and install it.

Creating package in ./BSgenome.dme.BDGP6.32
Loading '2L' sequence from FASTA file '/media/ken/BackUP/Drosophila/BSgenome/2L.fa' ... DONE
Loading '2R' sequence from FASTA file '/media/ken/BackUP/Drosophila/BSgenome/2R.fa' ... DONE
Loading '3L' sequence from FASTA file '/media/ken/BackUP/Drosophila/BSgenome/3L.fa' ... DONE
Loading '3R' sequence from FASTA file '/media/ken/BackUP/Drosophila/BSgenome/3R.fa' ... DONE
Loading '4' sequence from FASTA file '/media/ken/BackUP/Drosophila/BSgenome/4.fa' ... DONE
Loading 'EGFP' sequence from FASTA file '/media/ken/BackUP/Drosophila/BSgenome/EGFP.fa' ... DONE
Loading 'GAL4' sequence from FASTA file '/media/ken/BackUP/Drosophila/BSgenome/GAL4.fa' ... DONE
Loading 'mCD8GFP' sequence from FASTA file '/media/ken/BackUP/Drosophila/BSgenome/mCD8GFP.fa' ... DONE
Loading 'mitochondrion_genome' sequence from FASTA file '/media/ken/BackUP/Drosophila/BSgenome/mitochondrion_genome.fa' ... DONE
Loading 'test' sequence from FASTA file '/media/ken/BackUP/Drosophila/BSgenome/test.fa' ... DONE
Loading 'X' sequence from FASTA file '/media/ken/BackUP/Drosophila/BSgenome/X.fa' ... DONE
Loading 'Y' sequence from FASTA file '/media/ken/BackUP/Drosophila/BSgenome/Y.fa' ... DONE
Writing all sequences to './BSgenome.dme.BDGP6.32/inst/extdata/single_sequences.2bit' ... DONE

R CMD build BSgenome.dme.BDGP6.32
R CMD INSTALL BSgenome.dme.BDGP6.32_1.0.0.tar.gz

Now, you can load your Genome